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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $species_info = array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ) $local_species = 'cbr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $species_info = array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ) $local_species = 'cbr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $species_info = array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ) $local_species = 'cre' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $species_info = array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ) $local_species = 'cre' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $species_info = array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ) $local_species = 'mco' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $species_info = array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ) $local_species = 'mco' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $species_info = array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ) $local_species = 'pco' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $species_info = array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ) $local_species = 'pco' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ), 'gf_id' => 'HOM05D001120', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001120' ), 'data_identifier' => 'HOM05D001120', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001120', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p42180' => 'bna', 'A02p42190' => 'bna', 'A03p03110' => 'bna', 'A04p31640' => 'bna', 'A05p02300' => 'bna', 'A09p07570' => 'bna', 'A10p09590' => 'bna', 'A10p28950' => 'bna', 'Aa31LG11G1390' => 'aar', 'Aa31LG1G23490' => 'aar', 'Aa31LG3G19170' => 'aar', 'Aa31LG3G8190' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1247' => 'aag', 'Actinidia13529' => 'ach', 'Actinidia15780' => 'ach', 'Actinidia21986' => 'ach', 'Actinidia30541' => 'ach', 'Actinidia32913' => 'ach', 'Actinidia40472' => 'ach', 'Ah.13g067550' => 'amhyb', 'Ah.14g079790' => 'amhyb', 'AL4G39560' => 'aly', 'AL6G17410' => 'aly', 'AL8G26010' => 'aly', 'AL8G39020' => 'aly', 'AL8G39030' => 'aly', 'Aqoxy3G00121' => 'aox', 'Aqoxy5G03582' => 'aox', 'Aqoxy5G03662' => 'aox', 'Aqoxy5G03663' => 'aox', 'Aqoxy5G03732' => 'aox', 'Aqoxy5G03734' => 'aox', 'Aqoxy6G01992' => 'aox', 'Aqoxy7G00546' => 'aox', 'Aqoxy7G02184' => 'aox', 'Aqoxy7G03703' => 'aox', 'arahy.Tifrunner.gnm1.ann1.02H4Y5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0ZDL97' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.16TVZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1FS32P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1V5DEN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2Y8ZXL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35XLXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J2MYH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A2YXVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B50YZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BDNL9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4F5HJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I9RXZ3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LIRE4J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMQR93' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PGBG9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1XR2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W17802' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1WI1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM6BPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVWX7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZX35QI' => 'arhy', 'AT2G41475' => 'ath', 'AT5G07190' => 'ath', 'AT5G51740' => 'ath', 'AT5G62200' => 'ath', 'AT5G62210' => 'ath', 'ATR0594G007' => 'atr', 'ATR0757G141' => 'atr', 'ATR1120G157' => 'atr', 'Atru.chr1.2998' => 'acertr', 'Atru.chr1.603' => 'acertr', 'Atru.chr1.606' => 'acertr', 'Atru.chr1.607' => 'acertr', 'Atru.chr1.610' => 'acertr', 'AUR62016080' => 'cqu', 'AUR62021289' => 'cqu', 'BcaB01g06032' => 'bca', 'BcaB07g29789' => 'bca', 'BcaB07g29790' => 'bca', 'BcaB08g35521' => 'bca', 'BcaC03g18135' => 'bca', 'BcaC03g18137' => 'bca', 'BcaC04g20640' => 'bca', 'BcaC04g23423' => 'bca', 'BcaC06g32465' => 'bca', 'BcaC06g32466' => 'bca', 'BcaNung01406' => 'bca', 'BolC2t12263H' => 'bol', 'BolC2t12264H' => 'bol', 'BolC3t12894H' => 'bol', 'BolC3t18728H' => 'bol', 'BolC4t21914H' => 'bol', 'BolC4t28404H' => 'bol', 'BolC9t53757H' => 'bol', 'BolC9t56993H' => 'bol', 'BolC9t59674H' => 'bol', 'BraA02t09147Z' => 'bra', 'BraA02t09148Z' => 'bra', 'BraA03t09668Z' => 'bra', 'BraA04t18622Z' => 'bra', 'BraA05t19225Z' => 'bra', 'BraA10t43035Z' => 'bra', 'BraA10t44942Z' => 'bra', 'C02p62030' => 'bna', 'C02p62040' => 'bna', 'C03p03510' => 'bna', 'C03p64690' => 'bna', 'C04p02740' => 'bna', 'C04p69070' => 'bna', 'C09p08490' => 'bna', 'C09p41150' => 'bna', 'C09p69300' => 'bna', 'CAN.G1409.5' => 'can', 'CAN.G407.95' => 'can', 'CAN.G798.15' => 'can', 'CAN.G798.16' => 'can', 'CANSAT21G0609' => 'cansat', 'CANSAT21G2107' => 'cansat', 'CANSAT21G2509' => 'cansat', 'CANSAT56G0855' => 'cansat', 'CARHR136590' => 'chi', 'CARHR205950' => 'chi', 'CARHR205960' => 'chi', 'CARHR264600' => 'chi', 'CARHR275990' => 'chi', 'Carub.0004s2377' => 'cru', 'Carub.0006s0612' => 'cru', 'Carub.0008s1176' => 'cru', 'Carub.0008s2289' => 'cru', 'Carub.0008s2290' => 'cru', 'Ca_01081_v3' => 'car', 'Ca_10832_v3' => 'car', 'Ca_11072_v3' => 'car', 'Ca_19532_v3' => 'car', 'Ca_19537_v3' => 'car', 'Ca_19538_v3' => 'car', 'CBR_g433' => 'cbr', 'Cc02_g03730' => 'ccan', 'Cc02_g27570' => 'ccan', 'Cc04_g04230' => 'ccan', 'Cc06_g08490' => 'ccan', 'CDE06G2009' => 'cde', 'CDE11G0287' => 'cde', 'Cfa008242' => 'cfa', 'Cfa021686' => 'cfa', 'Ciclev10004987m.g' => 'ccl', 'Ciclev10005897m.g' => 'ccl', 'Ciclev10006003m.g' => 'ccl', 'Ciclev10009669m.g' => 'ccl', 'Ciclev10026660m.g' => 'ccl', 'CiPaw.03G098300' => 'cil', 'CiPaw.03G098500' => 'cil', 'ClCG05G007550' => 'cla', 'ClCG05G007560' => 'cla', 'ClCG05G007570' => 'cla', 'ClCG05G007580' => 'cla', 'ClCG05G007590' => 'cla', 'ClCG07G012680' => 'cla', 'COL.COLO4_03392' => 'col', 'COL.COLO4_05154' => 'col', 'COL.COLO4_05155' => 'col', 'COL.COLO4_05156' => 'col', 'COL.COLO4_05158' => 'col', 'COL.COLO4_12579' => 'col', 'COL.COLO4_12943' => 'col', 'COL.COLO4_14202' => 'col', 'COL.COLO4_14203' => 'col', 'COL.COLO4_30184' => 'col', 'COL.COLO4_33195' => 'col', 'COL.COLO4_33196' => 'col', 'Cpa.g.sc3.252' => 'cpa', 'Cpa.g.sc3.254' => 'cpa', 'Cpa.g.sc75.26' => 'cpa', 'Cre06.g306650' => 'cre', 'Cre12.g552001' => 'cre', 'CsaV3_3G016450' => 'csa', 'CsaV3_3G016460' => 'csa', 'CsaV3_3G016470' => 'csa', 'CsaV3_4G001510' => 'csa', 'CSS0023912' => 'camsi', 'CSS0024775' => 'camsi', 'CSS0025134' => 'camsi', 'CSS0048333' => 'camsi', 'CSS0048489' => 'camsi', 'DCAR_007088' => 'dca', 'DCAR_018133' => 'dca', 'DCAR_025505' => 'dca', 'DCAR_032343' => 'dca', 'Dinv08003' => 'din', 'Dinv28521' => 'din', 'Duzib068G1270' => 'dzi', 'Duzib084G0294' => 'dzi', 'Duzib084G0753' => 'dzi', 'Duzib192G0269' => 'dzi', 'Duzib235G0839' => 'dzi', 'ECA232G3997' => 'eca', 'ECA233G0610' => 'eca', 'ECA233G6122' => 'eca', 'EL10Ac3g05113' => 'bvu', 'EL10Ac3g05114' => 'bvu', 'EL10Ac3g05115' => 'bvu', 'EL10Ac3g05116' => 'bvu', 'EL10Ac3g05117' => 'bvu', 'EL10Ac3g05118' => 'bvu', 'EL10Ac3g05764' => 'bvu', 'EL10Ac8g18658' => 'bvu', 'Eucgr.A02865' => 'egr', 'Eucgr.A02866' => 'egr', 'Eucgr.A02867' => 'egr', 'Eucgr.F02528' => 'egr', 'Eucgr.J03061' => 'egr', 'FAN01G0606' => 'fan', 'FAN02G1869' => 'fan', 'FAN03G0491' => 'fan', 'FAN03G1503' => 'fan', 'FAN03G1813' => 'fan', 'FAN03G1927' => 'fan', 'FAN05G2553' => 'fan', 'FAN06G0193' => 'fan', 'FAN06G0604' => 'fan', 'FAN06G0686' => 'fan', 'FAN06G2540' => 'fan', 'FAN06G2717' => 'fan', 'FAN06G3100' => 'fan', 'FAN06G4681' => 'fan', 'FAN06G4829' => 'fan', 'FAN09G4531' => 'fan', 'FAN10G0638' => 'fan', 'FAN10G1418' => 'fan', 'FAN10G3067' => 'fan', 'FAN20G0598' => 'fan', 'FvH4_6g29960' => 'fve', 'FvH4_7g28400' => 'fve', 'FvH4_7g28430' => 'fve', 'FvH4_7g28431' => 'fve', 'FvH4_7g28432' => 'fve', 'Glyma.06G289600' => 'gma', 'Glyma.09G151800' => 'gma', 'Glyma.09G151900' => 'gma', 'Glyma.10G242000' => 'gma', 'Glyma.12G117400' => 'gma', 'Glyma.13G363800' => 'gma', 'Glyma.13G364801' => 'gma', 'Glyma.15G008800' => 'gma', 'Glyma.16G202000' => 'gma', 'Glyma.16G202500' => 'gma', 'Glyma.20G152100' => 'gma', 'Gohir.A05G125700' => 'ghi', 'Gohir.A05G125866' => 'ghi', 'Gohir.A07G039900' => 'ghi', 'Gohir.A09G178700' => 'ghi', 'Gohir.D05G126700' => 'ghi', 'Gohir.D07G044000' => 'ghi', 'Gohir.D09G174300' => 'ghi', 'Gohir.D12G263833' => 'ghi', 'Gorai.001G047100' => 'gra', 'Gorai.006G196300' => 'gra', 'Gorai.008G282900' => 'gra', 'Gorai.009G130700' => 'gra', 'GSVIVG01018475001' => 'vvi', 'GSVIVG01018477001' => 'vvi', 'GSVIVG01018478001' => 'vvi', 'HanXRQChr02g0052421' => 'han', 'HanXRQChr03g0061581' => 'han', 'HanXRQChr04g0116241' => 'han', 'HanXRQChr05g0141341' => 'han', 'HanXRQChr10g0303001' => 'han', 'Haze_13809' => 'cav', 'Haze_13811' => 'cav', 'Hma1.2p1_0018F.1_g012390' => 'hma', 'Hma1.2p1_0033F.1_g020890' => 'hma', 'Hma1.2p1_0488F.1_g163780' => 'hma', 'Hma1.2p1_0515F.1_g170130' => 'hma', 'HPP92_000668' => 'vpl', 'HPP92_007982' => 'vpl', 'Hund04661' => 'sun', 'Hund09243' => 'sun', 'Hund11789' => 'sun', 'Lalb_Chr03g0033001' => 'lal', 'Lalb_Chr03g0033011' => 'lal', 'Lalb_Chr06g0160841' => 'lal', 'Lalb_Chr19g0131251' => 'lal', 'Lalb_Chr22g0350891' => 'lal', 'Lalb_Chr22g0350901' => 'lal', 'Lalb_Chr25g0289251' => 'lal', 'Lj2g0010051' => 'lja', 'Lj2g0018359' => 'lja', 'Lj3g0003878' => 'lja', 'Lj3g0018692' => 'lja', 'Lj5C70T11' => 'lonja', 'Lj6g0021937' => 'lja', 'Lj8C35G5' => 'lonja', 'Lsat_1_v5_gn_4_88960' => 'lsa', 'Lsat_1_v5_gn_4_89020' => 'lsa', 'Lsat_1_v5_gn_5_131260' => 'lsa', 'Lsat_1_v5_gn_8_157341' => 'lsa', 'Lsat_1_v5_gn_8_7961' => 'lsa', 'Manes.04G114400' => 'mes', 'Manes.06G139500' => 'mes', 'Manes.14G031901' => 'mes', 'Manes.14G132300' => 'mes', 'Mapoly0030s0021' => 'mpo', 'MBI04_g38656_MAGBIO' => 'mbi', 'MBI12_g37712_MAGBIO' => 'mbi', 'MBI14_g46136_MAGBIO' => 'mbi', 'MCO09G181' => 'mco', 'MD00G1023000' => 'mdo', 'MD00G1023100' => 'mdo', 'MD01G1187700' => 'mdo', 'MD01G1187900' => 'mdo', 'MD02G1031500' => 'mdo', 'MD07G1015000' => 'mdo', 'MD07G1259800' => 'mdo', 'MD07G1260500' => 'mdo', 'MD07G1261400' => 'mdo', 'Medtr0050s0240' => 'mtr', 'Medtr1g012010' => 'mtr', 'Medtr1g012015' => 'mtr', 'Medtr1g014390' => 'mtr', 'Medtr1g029560' => 'mtr', 'Medtr1g102420' => 'mtr', 'Medtr2g103303' => 'mtr', 'Medtr2g103307' => 'mtr', 'Medtr2g103313' => 'mtr', 'Medtr2g103330' => 'mtr', 'Medtr2g103360' => 'mtr', 'Medtr2g103670' => 'mtr', 'Medtr3g006860' => 'mtr', 'Medtr6g006710' => 'mtr', 'Medtr6g006850' => 'mtr', 'Medtr6g061650' => 'mtr', 'Medtr6g079410' => 'mtr', 'Medtr6g079950' => 'mtr', 'Medtr6g080120' => 'mtr', 'Medtr6g463380' => 'mtr', 'Medtr7g025575' => 'mtr', 'Medtr7g405760' => 'mtr', 'MELO3C006843.2' => 'cme', 'MELO3C006844.2' => 'cme', 'MELO3C006845.2' => 'cme', 'MELO3C006846.2' => 'cme', 'MELO3C017889.2' => 'cme', 'MELO3C032675.2' => 'cme', 'Migut.F01165' => 'egut', 'Migut.I00781' => 'egut', 'Migut.K00480' => 'egut', 'MSTRG.22732' => 'ama', 'MSTRG.27147' => 'ama', 'Nitab4.5_0000024g0220' => 'nta', 'Nitab4.5_0000072g0150' => 'nta', 'Nitab4.5_0001250g0010' => 'nta', 'Nitab4.5_0006353g0020' => 'nta', 'Nn1g01163' => 'nnu', 'Nn2g10579' => 'nnu', 'Nn2g12032' => 'nnu', 'Nn4g25984' => 'nnu', 'Nn8g39453' => 'nnu', 'Oeu021740.1' => 'oeu', 'Oeu049186.1' => 'oeu', 'Os01g0172800' => 'osa', 'Os02g0735100' => 'osa', 'Os05g0171200' => 'osa', 'Peaxi162Scf00148g00114' => 'pax', 'Peaxi162Scf00192g00835' => 'pax', 'Peaxi162Scf00332g00768' => 'pax', 'PGR031G1653' => 'pgr', 'PGR042G0858' => 'pgr', 'PGR042G1649' => 'pgr', 'PGSC0003DMG400000634' => 'stu', 'PGSC0003DMG400023797' => 'stu', 'PGSC0003DMG400023798' => 'stu', 'PGSC0003DMG400031017' => 'stu', 'Phvul.004G125300' => 'pvu', 'Phvul.004G125400' => 'pvu', 'Phvul.004G125600' => 'pvu', 'Phvul.005G175450' => 'pvu', 'Phvul.005G177100' => 'pvu', 'Phvul.007G063600' => 'pvu', 'Phvul.011G124600' => 'pvu', 'Potri.001G193500' => 'ptr', 'Potri.006G069800' => 'ptr', 'Potri.012G130800' => 'ptr', 'Potri.012G130900' => 'ptr', 'Potri.012G131100' => 'ptr', 'Potri.015G132700' => 'ptr', 'Potri.015G132900' => 'ptr', 'Potri.018G131800' => 'ptr', 'Pp3c23_3440' => 'ppa', 'PRCOL_00000894' => 'pco', 'Prupe.2G222000' => 'ppe', 'Prupe.2G284100' => 'ppe', 'Prupe.2G284300' => 'ppe', 'Prupe.2G284400' => 'ppe', 'Prupe.3G084200' => 'ppe', 'Prupe.7G243200' => 'ppe', 'Psat1g105640' => 'psa', 'Psat1g115720' => 'psa', 'Psat5g300280' => 'psa', 'Psat5g300320' => 'psa', 'Psat5g300880' => 'psa', 'Psat5g300920' => 'psa', 'Psat5g300960' => 'psa', 'Psat5g301440' => 'psa', 'Psat5g301880' => 'psa', 'Psat6g203680' => 'psa', 'Psat7g030920' => 'psa', 'PSO170G1098' => 'pso', 'PSO210G7235' => 'pso', 'PSO339G5748' => 'pso', 'PSO384G0990' => 'pso', 'PSO455G0274' => 'pso', 'PSO478G1088' => 'pso', 'PSO478G1122' => 'pso', 'PSO478G1970' => 'pso', 'PSO478G4258' => 'pso', 'PSO782G1143' => 'pso', 'PSO782G3773' => 'pso', 'PSO832G4332' => 'pso', 'QL01p011565' => 'qlo', 'QL05p028937' => 'qlo', 'QL08p051844' => 'qlo', 'QL08p051863' => 'qlo', 'QL12p022862' => 'qlo', 'QL12p023764' => 'qlo', 'QL12p039195' => 'qlo', 'QL12p039198' => 'qlo', 'QL12p039215' => 'qlo', 'RcHm_v2.0_Chr1g0375361' => 'rch', 'RcHm_v2.0_Chr1g0375381' => 'rch', 'RcHm_v2.0_Chr1g0375391' => 'rch', 'RcHm_v2.0_Chr1g0375401' => 'rch', 'RcHm_v2.0_Chr1g0375411' => 'rch', 'RcHm_v2.0_Chr2g0123811' => 'rch', 'RcHm_v2.0_Chr2g0135961' => 'rch', 'RcHm_v2.0_Chr4g0391111' => 'rch', 'RcHm_v2.0_Chr4g0406741' => 'rch', 'Rhsim03G0173300' => 'rsi', 'Rhsim05G0178800' => 'rsi', 'Rhsim07G0024900' => 'rsi', 'Rhsim07G0025100' => 'rsi', 'Rhsim07G0025300' => 'rsi', 'Rhsim07G0026200' => 'rsi', 'Rhsim08G0214200' => 'rsi', 'Rhsim09G0194100' => 'rsi', 'Sabra06G0052100' => 'sbr', 'Sabra12G0098500' => 'sbr', 'Sabra12G0098600' => 'sbr', 'Sabra15G0145300' => 'sbr', 'Sabra15G0145600' => 'sbr', 'SalBow2G0050' => 'sbo', 'SalBow2G1796' => 'sbo', 'Sc04g0004600' => 'sci', 'Sc18g0000610' => 'sci', 'Sc19g0001810' => 'sci', 'Sed0000479' => 'sed', 'Sed0008007' => 'sed', 'Sed0010780' => 'sed', 'Sed0018265' => 'sed', 'Sed0023521' => 'sed', 'Sed0024680' => 'sed', 'SEGI_17058' => 'sgi', 'SEGI_40718' => 'sgi', 'SGA_v2.0_scaffold106G30701' => 'sas', 'SGA_v2.0_scaffold10G05437' => 'sas', 'SGA_v2.0_scaffold10G05473' => 'sas', 'SGA_v2.0_scaffold14G06826' => 'sas', 'SGA_v2.0_scaffold337G49175' => 'sas', 'SGA_v2.0_scaffold43G16464' => 'sas', 'SGA_v2.0_scaffold43G16465' => 'sas', 'SGA_v2.0_scaffold4G02419' => 'sas', 'SGA_v2.0_scaffold51G18691' => 'sas', 'SGA_v2.0_scaffold5G02678' => 'sas', 'SMO172G0194' => 'smo', 'Solyc01g104020.2' => 'sly', 'Solyc03g007000.4' => 'sly', 'Solyc03g116590.3' => 'sly', 'Sopen01g046420' => 'spe', 'Sopen01g046430' => 'spe', 'Sopen03g003000' => 'spe', 'Sopen03g035500' => 'spe', 'Sp2g25400' => 'spa', 'Sp2g25410' => 'spa', 'Sp4g23740' => 'spa', 'Sp6g13950' => 'spa', 'Sp6g13960' => 'spa', 'Sp6g35700' => 'spa', 'Sp6g35710' => 'spa', 'TAR375G0839' => 'tar', 'TAR383G0395' => 'tar', 'TAR645G0001' => 'tar', 'TAR645G0006' => 'tar', 'THA.LOC104798865' => 'tha', 'THA.LOC104806528' => 'tha', 'THA.LOC104811503' => 'tha', 'THA.LOC104815278' => 'tha', 'THA.LOC104824839' => 'tha', 'THA.LOC104824840' => 'tha', 'THA.LOC104825077' => 'tha', 'THA.LOC104825078' => 'tha', 'THA.LOC104825079' => 'tha', 'THA.LOC104825082' => 'tha', 'THA.LOC104825185' => 'tha', 'THA.LOC104825186' => 'tha', 'Thecc.03G163700' => 'tca', 'Thecc.03G163900' => 'tca', 'Thecc.06G021100' => 'tca', 'Thhalv10004875m.g' => 'esa', 'Thhalv10004970m.g' => 'esa', 'Thhalv10013554m.g' => 'esa', 'Thhalv10015927m.g' => 'esa', 'Thhalv10015930m.g' => 'esa', 'Thhalv10017295m.g' => 'esa', 'TPR.G15608' => 'tpr', 'TPR.G24658' => 'tpr', 'TPR.G26127' => 'tpr', 'TPR.G26586' => 'tpr', 'TPR.G26589' => 'tpr', 'TPR.G31349' => 'tpr', 'TPR.G33098' => 'tpr', 'TPR.G36381' => 'tpr', 'TPR.G37157' => 'tpr', 'TPR.G37165' => 'tpr', 'TPR.G37175' => 'tpr', 'TPR.G37183' => 'tpr', 'TPR.G37187' => 'tpr', 'TPR.G37267' => 'tpr', 'TPR.G37272' => 'tpr', 'TPR.G608' => 'tpr', 'TPR.G7033' => 'tpr', 'TPR.G7034' => 'tpr', 'TWI18G0686' => 'twi', 'TWI23G0455' => 'twi', 'TWI23G0697' => 'twi', 'unitig_22.g6612' => 'ugi', 'unitig_26.g9851' => 'ugi', 'unitig_52.g17752' => 'ugi', 'unitig_92.g28179' => 'ugi', 'unitig_92.g28185' => 'ugi', 'unitig_92.g28221' => 'ugi', 'unitig_92.g28224' => 'ugi', 'vmacro06755' => 'vma', 'vmacro06756' => 'vma', 'vmacro09881' => 'vma', 'vmacro13381' => 'vma', 'vmacro18984' => 'vma', 'VMungo0464G0810' => 'vmu', 'VMungo0464G0837' => 'vmu', 'VMungo0464G2024' => 'vmu', 'VMungo0720G0371' => 'vmu', 'VMungo1127G0245' => 'vmu', 'Zm00001eb253810' => 'zma', 'Zm00001eb336790' => 'zma' ) $gf_id = 'HOM05D001120' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001120' ) $data_identifier = 'HOM05D001120' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 10, 'arhy' => (int) 22, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 2, 'bca' => (int) 11, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 2, 'cla' => (int) 6, 'col' => (int) 12, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 8, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 5, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 22, 'cme' => (int) 6, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 4, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 8, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 11, 'pso' => (int) 12, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 8, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 10, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 12, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 18, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb336790' $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